GapMind for catabolism of small carbon sources

 

D-xylose catabolism

Analysis of pathway xylose in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 xylT, xylA, xylB
Acidithiobacillus ferrooxidans ATCC 23270 xylT, xylA, xylB
Acidovorax sp. GW101-3H11 xylF, xylG, xylH, xdh, xylC, xad, kdaD, dopDH
Algiphilus aromaticivorans DG1253 xylT, xylA, xylB
Alicycliphilus denitrificans K601 xylT, xylA, xylB
Alkalihalobacterium alkalinitrilicum DSM 22532 xylT, xylA, xylB
Allochromatium vinosum DSM 180 xylT, xylA, xylB
Ammonifex degensii KC4 xylT, xylA, xylB
Anaerobutyricum hallii DSM 3353 xylT, xylA, xylB
Aquimarina longa SW024 Echvi_1871, xylA, xylB
Archaeoglobus veneficus SNP6 xylT, xylA, xylB
Arcobacter nitrofigilis DSM 7299 xylT, xylA, xylB
Azoarcus olearius BH72 xylT, xylA, xylB
Azohydromonas australica DSM 1124 gtsA, gtsB, gtsC, gtsD, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Azorhizobium caulinodans ORS 571 xylT, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Azospirillum brasilense Sp245 xylF, xylG, xylH, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Azospirillum sp. B510 xylF, xylG, xylH, xylA, xylB
Bacteroides thetaiotaomicron VPI-5482 xylT, xylA, xylB
Beijerinckia indica ATCC 9039 xylF, xylG, xylH, xyrA, xdhA, xylB
Beijerinckia mobilis UQM 1969 xylT, xylA, xylB
Billgrantia desiderata SP1 xylT, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Bradyrhizobium sp. BTAi1 xylF, xylG, xylH, xylA, xylB
Brevundimonas sp. GW460-12-10-14-LB2 xylT, xdh, xylC, xad, kdaD, dopDH
Burkholderia phytofirmans PsJN xylF, xylG, xylH, xylA, xylB
Burkholderia vietnamiensis G4 xylF, xylG, xylH, xylA, xylB
Calditerrivibrio nitroreducens DSM 19672 xylT, xylA, xylB
Caminibacter mediatlanticus TB-2 xylT, xylA, xylB
Carboxydothermus pertinax Ug1 xylT, xylA, xylB
Caulobacter crescentus NA1000 xylT, xdh, xylC, xad, kdaD, dopDH
Cereibacter sphaeroides ATCC 17029 xylT, xylA, xylB
Chlorobaculum parvum NCIB 8327 xylT, xylA, xylB
Chlorobaculum tepidum TLS xylT, xylA, xylB
Chlorobium limicola DSM 245 xylT, xylA, xylB
Chlorobium phaeobacteroides BS1 xylT, xylA, xylB
Clostridium acetobutylicum ATCC 824 xylT, xylA, xylB
Clostridium kluyveri DSM 555 xylT, xylA, xylB
Clostridium tyrobutyricum FAM22553 xylT, xylA, xylB
Crocosphaera subtropica ATCC 51142 xylT, xylA, xylB
Cupriavidus basilensis FW507-4G11 xylF, xylG, xylH, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Dechloromonas agitata is5 xylT, xylA, xylB
Dechlorosoma suillum PS xylT, xylA, xylB
Dehalococcoides mccartyi 195 xylT, xylA, xylB
Denitrovibrio acetiphilus DSM 12809 xylT, xylA, xylB
Derxia gummosa DSM 723 gtsA, gtsB, gtsC, gtsD, xylA, xylB
Desulfacinum hydrothermale DSM 13146 xylT, xylA, xylB
Desulfacinum infernum DSM 9756 xylT, xylA, xylB
Desulfarculus baarsii DSM 2075 xylT, xylA, xylB
Desulfatibacillum aliphaticivorans DSM 15576 xylT, xylA, xylB
Desulfatiglans anilini DSM 4660 xylT, xylA, xylB
Desulfitobacterium hafniense DCB-2 xylT, xylA, xylB
Desulfobacca acetoxidans DSM 11109 xylT, xylA, xylB
Desulfobacter vibrioformis DSM 8776 xylT, xylA, xylB
Desulfogranum mediterraneum DSM 13871 xylF, xylG, xylH, xylA, xylB
Desulforamulus ruminis DSM 2154 xylT, xyrA, xdhA, xylB
Desulfoscipio geothermicus DSM 3669 xylT, xylA, xylB
Desulfotalea psychrophila LSv54 xylT, xylA, xylB
Desulfovibrio oxyclinae DSM 11498 xylT, xylA, xylB
Desulfovibrio vulgaris Hildenborough JW710 xylT, xylA, xylB
Desulfovibrio vulgaris Miyazaki F xylT, xylA, xylB
Desulfurobacterium atlanticum DSM 15668 xylT, xylA, xylB
Desulfuromonas acetexigens xylT, xylA, xylB
Desulfuromusa kysingii DSM 7343 xylT, xylA, xylB
Dinoroseobacter shibae DFL-12 xylT, xylA, xylB
Dyella japonica UNC79MFTsu3.2 xylF, xylG, xylH, xylA, xylB
Echinicola vietnamensis KMM 6221, DSM 17526 Echvi_1871, xylA, xylB
Escherichia coli BW25113 xylF, xylG, xylH, xylA, xylB
Ferroglobus placidus DSM 10642 xylT, xylA, xylB
Frankia alni ACN14a xylT, xylA, xylB
Geobacter metallireducens GS-15 xylT, xylA, xylB
Geotalea uraniireducens Rf4 xylT, xylA, xylB
Halococcus hamelinensis 100A6 xylT, xdh, xylC, xad, kdaD, dopDH
Haloechinothrix alba DSM 45207 xylT, xyrA, xdhA, xylB
Haloferax volcanii DS2 xylT, xdh, xylC, xad, kdaD, dopDH
Haloglycomyces albus DSM 45210 xylF, xylG, xylH, xylA, xylB
Halorhodospira halophila SL1 xylT, xylA, xylB
Heliomicrobium modesticaldum Ice1; ATCC 51547 xylT, xylA, xylB
Herbaspirillum autotrophicum IAM 14942 xylT, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Herbaspirillum seropedicae SmR1 xylF, xylG, xylH, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Hippea alviniae EP5-r xylT, xylA, xylB
Hydrogenophaga taeniospiralis NBRC 102512 xylF, xylG, xylH, xylA, xylB
Hydrogenovibrio halophilus DSM 15072 xylT, xylA, xylB
Hydrogenovibrio kuenenii DSM 12350 xylT, xylA, xylB
Hydrogenovibrio marinus DSM 11271 xylT, xylA, xylB
Hyphomicrobium sulfonivorans WDL6 xylT, xylA, xylB
Klebsiella michiganensis M5al xylF, xylG, xylH, xylA, xylB
Klebsiella variicola At-22 xylF, xylG, xylH, xylA, xylB
Kyrpidia tusciae DSM 2912 xylT, xylA, xylB
Leptospirillum ferrooxidans C2-3 xylT, xylA, xylB
Magnetospirillum magneticum AMB-1 xylT, xylA, xylB
Malonomonas rubra DSM 5091 xylT, xylA, xylB
Maridesulfovibrio bastinii DSM 16055 xylT, xylA, xylB
Maridesulfovibrio zosterae DSM 11974 xylT, xylA, xylB
Marinobacter adhaerens HP15 gtsA, gtsB, gtsC, gtsD, xylA, xylB
Mesorhizobium ciceri WSM1271 xylF, xylG, xylH, xylA, xylB
Methanobacterium lacus AL-21 xylT, xylA, xylB
Methanococcus aeolicus Nankai-3 xylT, xylA, xylB
Methanococcus maripaludis C5 xylT, xylA, xylB
Methanosarcina acetivorans C2A xylT, xylA, xylB
Methanosarcina mazei Go1 xylT, xylA, xylB
Methanospirillum lacunae Ki8-1 xylT, xylA, xylB
Methanothermobacter thermautotrophicus Delta H xylT, xylA, xylB
Methylobacterium nodulans ORS 2060 xylT, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Methylobacterium sp. 4-46 Apr-46 xylT, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Methylocapsa acidiphila B2 xylT, xylA, xylB
Methylocapsa aurea KYG xylT, xylA, xylB
Methylocella silvestris BL2 xylT, xylA, xylB
Methylococcus capsulatus Bath xylT, xylA, xylB
Methylocystis bryophila S285 xylT, xylA, xylB
Methyloferula stellata AR4T xylT, xylA, xylB
Methylohalobius crimeensis 10Ki xylT, xylA, xylB
Methylomonas methanica MC09 xylT, xylA, xylB
Methylosarcina fibrata AML-C10 xylT, xylA, xylB
Methylotuvimicrobium alcaliphilum 20Z xylT, xylA, xylB
Methylovulum miyakonense HT12 xylT, xylA, xylB
Mycolicibacterium vanbaalenii PYR-1 xylT, xylA, xylB
Nitratifractor salsuginis DSM 16511 xylT, xylA, xylB
Nitratiruptor tergarcus DSM 16512 xylT, xylA, xylB
Nitriliruptor alkaliphilus DSM 45188 xylF, xylG, xylH, xylA, xylB
Nocardioides dokdonensis FR1436 xylT, xylA, xylB
Nocardiopsis lucentensis DSM 44048 xylT, xyrA, xdhA, xylB
Nostoc punctiforme ATCC 29133; PCC 73102 xylT, xyrA, xdhA, xylB
Novosphingobium aromaticivorans DSM 12444 xylT, xylA, xylB
Oleispira antarctica xylT, xylA, xylB
Paraburkholderia atlantica CCGE1002 xylF, xylG, xylH, xdh, xylC, xad, kdaD, dopDH
Paraburkholderia bryophila 376MFSha3.1 xylF, xylG, xylH, xylA, xylB
Paraburkholderia phymatum STM815 xylF, xylG, xylH, xylA, xylB
Paucidesulfovibrio gracilis DSM 16080 xylT, xylA, xylB
Pedobacter sp. GW460-11-11-14-LB5 xylT, xylA, xylB
Pelobacter propionicus DSM 2379 xylT, xylA, xylB
Persephonella marina EX-H1 xylT, xylA, xylB
Phaeacidiphilus oryzae TH49 xylT, xylA, xylB
Phaeobacter inhibens BS107 xylF, xylG, xylH, xylA, xylB
Polaromonas naphthalenivorans CJ2 gtsA, gtsB, gtsC, gtsD, xylA, xylB
Prosthecochloris aestuarii DSM 271 xylT, xylA, xylB
Pseudarthrobacter sulfonivorans Ar51 xylF, xylG, xylH, xylA, xylB
Pseudomonas benzenivorans DSM 8628 gtsA, gtsB, gtsC, gtsD, xylA, xylB
Pseudomonas fluorescens FW300-N1B4 gtsA, gtsB, gtsC, gtsD, xylA, xylB
Pseudomonas fluorescens FW300-N2C3 xylF, xylG, xylH, xylA, xylB
Pseudomonas fluorescens FW300-N2E2 xylF, xylG, xylH, xylA, xylB
Pseudomonas fluorescens FW300-N2E3 gtsA, gtsB, gtsC, gtsD, xylA, xylB
Pseudomonas fluorescens GW456-L13 gtsA, gtsB, gtsC, gtsD, xylA, xylB
Pseudomonas putida KT2440 gtsA, gtsB, gtsC, gtsD, xdh, xylC, xad, kdaD, dopDH
Pseudomonas simiae WCS417 gtsA, gtsB, gtsC, gtsD, xylA, xylB
Pseudomonas stutzeri RCH2 gtsA, gtsB, gtsC, gtsD, xylA, xylB
Pyrolobus fumarii 1A xylT, xylA, xylB
Rhizobium etli CFN 42 xylF, xylG, xylH, xylA, xylB
Rhizobium johnstonii 3841 xylF, xylG, xylH, xylA, xylB
Rhizobium leguminosarum WSM1325 xylF, xylG, xylH, xylA, xylB
Rhizorhabdus wittichii RW1 xylT, xylA, xylB
Rhodanobacter denitrificans FW104-10B01 xylT, xylA, xylB
Rhodomicrobium vannielii ATCC 17100 xylT, xylA, xylB
Rhodopseudomonas palustris CGA009 xylT, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Rhodospirillum centenum SW; ATCC 51521 xylT, xylA, xylB
Rhodospirillum rubrum ATCC 11170 gtsA, gtsB, gtsC, gtsD, xyrA, xdhA, xylB
Roseburia faecis M72 xylT, xylA, xylB
Saccharomonospora cyanea NA-134 xylT, xylA, xylB
Sedimenticola selenatireducens DSM 17993 xylT, xylA, xylB
Shewanella amazonensis SB2B xylT, xylA, xylB
Shewanella loihica PV-4 Echvi_1871, xylA, xylB
Shewanella oneidensis MR-1 xylT, xylA, xylB
Shewanella sp. ANA-3 xylT, xylA, xylB
Sinorhizobium fredii NGR234 xylF, xylG, xylH, xylA, xylB
Sinorhizobium medicae WSM419 xylF, xylG, xylH, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Sinorhizobium meliloti 1021 xylF, xylG, xylH, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Sphingomonas koreensis DSMZ 15582 xylT, xdh, xylC, xad, kdaD, dopDH
Stenotrophomonas chelatiphaga DSM 21508 xylT, xylA, xylB
Steroidobacter denitrificans DSM 18526 xylT, xylA, xylB
Stutzerimonas stutzeri A1501 gtsA, gtsB, gtsC, gtsD, xylA, xylB
Sulfuricurvum kujiense DSM 16994 xylT, xylA, xylB
Sulfurihydrogenibium azorense Az-Fu1 xylT, xylA, xylB
Sulfurihydrogenibium subterraneum DSM 15120 xylT, xylA, xylB
Sulfurimonas denitrificans DSM 1251 xylT, xylA, xylB
Sulfuritalea hydrogenivorans DSM 22779 xylT, xylA, xylB
Sulfurivirga caldicuralii DSM 17737 xylT, xylA, xylB
Synechococcus elongatus PCC 7942 xylT, xylA, xylB
Teredinibacter turnerae T7901 xylT, xylA, xylB
Thauera aminoaromatica S2 xylT, xylA, xylB
Thermithiobacillus tepidarius DSM 3134 xylT, xylA, xylB
Thermocrinis albus DSM 14484 xylT, xylA, xylB
Thermodesulforhabdus norvegica DSM 9990 xylT, xylA, xylB
Thermomonospora curvata DSM 43183 xylT, xylA, xylB
Thermovibrio ammonificans HB-1 xylT, xylA, xylB
Thermus aquaticus YT-1 xylT, xylA, xylB
Thioalkalivibrio denitrificans ALJD xylT, xylA, xylB
Thioalkalivibrio halophilus HL17 xylT, xylA, xylB
Thioalkalivibrio paradoxus ARh 1 xylT, xylA, xylB
Thioalkalivibrio thiocyanodenitrificans ARhD 1 xylT, xylA, xylB
Thiohalomonas denitrificans HLD2 xylT, xylA, xylB
Thiohalospira halophila HL 3 xylT, xylA, xylB
Thiomicrorhabdus arctica DSM 13458 xylT, xylA, xylB
Thiomicrorhabdus chilensis DSM 12352 xylT, xylA, xylB
Thiomicrospira cyclica ALM1 xylT, xylA, xylB
Thiomicrospira microaerophila ASL8-2 xylT, xylA, xylB
Thiomicrospira pelophila DSM 1534 xylT, xylA, xylB
Thiothrix lacustris DSM 21227 xylT, xylA, xylB
Tistlia consotensis USBA 355 xylF, xylG, xylH, xdh, xylC, xad, kdaD, dopDH
Trichlorobacter lovleyi SZ xylT, xylA, xylB
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome xylT, xylA, xylB
Trichormus variabilis ATCC 29413 xylF, xylG, xylH, xylA, xylB
Xanthobacter autotrophicus Py2 xylT, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Xenophilus azovorans DSM 13620 xylT, xdh, xylC, xad, kdaD, dopDH

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory